Humanize
This tab provides an alternative view of unusual residues and residue distributions to aid in humanization, de-immunization and optimization studies.
Global Viewing Options
Three selection boxes are included at the top-right of the page to customize the display all tabs in the Key Annotation section as indicated in the Summary Tab.
The heatmap display
The first two rows of the table show the abYsis numbering for the sequence based on the selected numbering scheme.
The main display shows residue frequencies as a 'heatmap'. Each horizontal position represents an amino acid along the sequence while each vertical column can be thought of as looking down on the relevant distribution graph for the Target Organism seeing high peaks (common residues) in green, medium peaks in yellow and low peaks (unusual residues) in red.
The CDRs (based on the selected CDR definition) are indicated with slightly darker colours.
The first row displays the sequence of interest coloured by reference to the Source Organism. Typically you would set this to your donor species (e.g. mouse).
The second row (and the heatmap below it) colours residues based on the distributions seen in the Target Organism. Normally you would set this to your acceptor species (typically human).
The next row gives a condensed view of the Germline display. This will be based parameters used on the Germline View tab, and will change based on settings in that page. Note that it is the translation, not the DNA, which is displayed here.
The next 20 rows are the main heatmap with distributions derived from the Target Organism. Common residues are shown in green; unusual residues are shown in red; other residues are shown in yellow.
Below the heatmap, the canonical class data are displayed in the same format as that of the Canonical Classes tab.
The secondary structure and solvent accessibility data are displayed below the canonical class data. These are displayed in the same format as the Canonical Classes tab and can be hidden and revealed in the same way. (See secondary structure and solvent accessibility).
The final row starts out as the same as the second row - i.e. the sequence of interest coloured by reference to the Source Organism.
Hovering over any heatmap cell will show crosshairs to aid location of the cell. In addition, for residues where the is an associated canonical class match or mismatch, the nature of replacement for each CDR is indicated by a popup.
Clicking on a residue in the heatmap will introduce the mutation to the sequence at the bottom of the heatmap, indicated by a lower-case residue label, updating the colour in that sequence appropriately.
Display controls
The Source Organism dropdown allows the organism to be selected which is used for colouring the sequence in the first row of the heatmap table.
The Target Organism dropdown allows the organism to be selected which is used for colouring the sequence in the second row of the heatmap table and in the main heatmap below it.
The Scaled / Not Scaled radio-buttons select whether the colouring of the heat map uses the raw percentage occurrence (Not Scaled) or the percentage occurrence with respect to the most common residue at that position (Scaled). For a particular position, if all residues are used equally then, without scaling, they would all have a frequency of 0.05; with scaling they would all have a frequency of 1.0.
The Lower limit / Upper limit boxes and associated two-handle slider allows you to specify the colouring thresholds. Residues having a frequency above the Upper limit will be green; residues having a frequency below the Lower limit will be red; residues having a frequency between the two limits will be yellow.
The guide cross hairs can be toggled on or off using the toggle button.
The Export button exports the mutated sequence to an Excel (XML) spreadsheet.
The button will change all mutated residues back to the original sequence.
Distribution graph and table
The distribution graph and table are displayed as indicated in the Summary tab section.
Clicking any residue in either of the top two rows will update the Distribution graph and table.